Maxent, one of the most commonly used methods for inferring species distributions and environmental tolerances from occurrence data, allows users to fit models of arbitrary complexity. Model ...complexity is typically constrained via a process known as
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regularization, but at present little guidance is available for setting the appropriate level of regularization, and the effects of inappropriately complex or simple models are largely unknown. In this study, we demonstrate the use of information criterion approaches to setting regularization in Maxent, and we compare models selected using information criteria to models selected using other criteria that are common in the literature. We evaluate model performance using occurrence data generated from a known "“true"” initial Maxent model, using several different metrics for model quality and transferability. We demonstrate that models that are inappropriately complex or inappropriately simple show reduced ability to infer habitat quality, reduced ability to infer the relative importance of variables in constraining species' distributions, and reduced transferability to other time periods. We also demonstrate that information criteria may offer significant advantages over the methods commonly used in the literature.
We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. The virus is more stable at low-temperature and low-humidity ...conditions, whereas warmer temperature and higher humidity shortened half-life. Although infectious virus was undetectable after 48 hours, viral RNA remained detectable for 7 days.
The coronavirus pandemic has created worldwide shortages of N95 respirators. We analyzed 4 decontamination methods for effectiveness in deactivating severe acute respiratory syndrome coronavirus 2 ...virus and effect on respirator function. Our results indicate that N95 respirators can be decontaminated and reused, but the integrity of respirator fit and seal must be maintained.
Most viral pathogens in humans have animal origins and arose through cross-species transmission. Over the past 50 years, several viruses, including Ebola virus, Marburg virus, Nipah virus, Hendra ...virus, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory coronavirus (MERS-CoV) and SARS-CoV-2, have been linked back to various bat species. Despite decades of research into bats and the pathogens they carry, the fields of bat virus ecology and molecular biology are still nascent, with many questions largely unexplored, thus hindering our ability to anticipate and prepare for the next viral outbreak. In this Review, we discuss the latest advancements and understanding of bat-borne viruses, reflecting on current knowledge gaps and outlining the potential routes for future research as well as for outbreak response and prevention efforts.
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic ...leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis. The infection was not cleared after the first treatment with convalescent plasma, suggesting a limited effect on SARS-CoV-2 in the upper respiratory tract of this individual. Several weeks after a second convalescent plasma transfusion, SARS-CoV-2 RNA was no longer detected. We observed marked within-host genomic evolution of SARS-CoV-2 with continuous turnover of dominant viral variants. However, replication kinetics in Vero E6 cells and primary human alveolar epithelial tissues were not affected. Our data indicate that certain immunocompromised individuals may shed infectious virus longer than previously recognized. Detection of subgenomic RNA is recommended in persistently SARS-CoV-2-positive individuals as a proxy for shedding of infectious virus.
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•Persistent SARS-CoV-2 infection and shedding in immunocompromised individual•Infectious SARS-CoV-2 isolated up to 70 days after diagnosis•Observed within-host genetic variation with continuous turnover of viral variants•SARS-CoV-2 isolates from the individual do not display altered replication
This case study describes a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia who became persistently infected with SARS-CoV-2. Although asymptomatic throughout the course of infection, she demonstrated prolonged shedding of infectious SARS-CoV-2 virus and RNA. This study demonstrates that certain individuals may remain infectious for prolonged periods of time and highlights the need for further studies to understand risk factors for prolonged infectious SARS-CoV-2 shedding.
Spillover of sarbecoviruses from animals to humans has resulted in outbreaks of severe acute respiratory syndrome SARS-CoVs and the ongoing COVID-19 pandemic. Efforts to identify the origins of ...SARS-CoV-1 and -2 has resulted in the discovery of numerous animal sarbecoviruses–the majority of which are only distantly related to known human pathogens and do not infect human cells. The receptor binding domain (RBD) on sarbecoviruses engages receptor molecules on the host cell and mediates cell invasion. Here, we tested the receptor tropism and serological cross reactivity for RBDs from two sarbecoviruses found in Russian horseshoe bats. While these two viruses are in a viral lineage distinct from SARS-CoV-1 and -2, the RBD from one virus, Khosta 2, was capable of using human ACE2 to facilitate cell entry. Viral pseudotypes with a recombinant, SARS-CoV-2 spike encoding for the Khosta 2 RBD were resistant to both SARS-CoV-2 monoclonal antibodies and serum from individuals vaccinated for SARS-CoV-2. Our findings further demonstrate that sarbecoviruses circulating in wildlife outside of Asia also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) likely originated in bats and passed to humans through dromedary camels; however, the genetic mechanisms underlying cross-species adaptation ...remain poorly understood. Variation in the host receptor, dipeptidyl peptidase 4 (DPP4), can block the interaction with the MERS-CoV spike protein and form a species barrier to infection. To better understand the species adaptability of MERS-CoV, we identified a suboptimal species-derived variant of DPP4 to study viral adaption. Passaging virus on cells expressing this DPP4 variant led to accumulation of mutations in the viral spike which increased replication. Parallel passages revealed distinct paths of viral adaptation to the same DPP4 variant. Structural analysis and functional assays showed that these mutations enhanced viral entry with suboptimal DPP4 by altering the surface charge of spike. These findings demonstrate that MERS-CoV spike can utilize multiple paths to rapidly adapt to novel species variation in DPP4.
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•MERS-CoV infected cells expressing DPP4 from 16 bat species•MERS-CoV spike rapidly adapted to species variation in DPP4•Viral adaptations modified the surface charge of viral spike•Different routes of spike adaptation enhanced entry with the same DPP4 variant
MERS-CoV is a zoonotic pathogen capable of infecting numerous species. However, our understanding of how this virus adapts to new species remains unclear. Letko et al. experimentally observe several different routes in the stepwise, adaptive evolution of MERS-CoV to a unique host-species variant of the viral receptor.
AIM: Ecological niche models are increasingly being used to aid in predicting the effects of future climate change on species distributions. Complex models that show high predictive performance on ...current distribution data may do a poor job of predicting new data due to overfitting. In addition, model performance is often evaluated using techniques that are sensitive to spatial sampling bias. Here, we explore the effects of model complexity and spatial sampling bias on niche models for 90 vertebrate taxa of conservation concern. LOCATION: California, USA. METHODS: We used Akaike information criterion (AICc) to select variables and tune Maxent's built‐in regularization parameter (β) to constrain model complexity. In addition, we incorporated several estimates of spatial sampling bias based on interpolations of target group data. Ensemble forecasts were developed for future conditions from two emission scenarios and three climate change models for the year 2050. RESULTS: Reducing the number of predictors and tuning β resulted in a reduction in the number of parameters in models built with sample sizes greater than approximately 10 occurrence points. Reducing the number of predictors had a substantially higher impact on the relative prioritization of different grid cells than did increasing regularization. There was little difference in prioritization of habitat when comparing models built using different spatial sampling bias estimates. Over half of the taxa were predicted to experience >80% reductions in environmental suitability in currently occupied cells, and this pattern was consistent across taxonomic groups. MAIN CONCLUSIONS: Our results demonstrate that reducing the number of correlated predictor variables tends to decrease the breadth of models, while tuning regularization using AICc tends to increase it. These two strategies may provide a reasonable bracketing strategy for assessing climate change impacts.
Most efforts to predict novel reservoirs of zoonotic pathogens use information about host exposure and infection rather than competence, defined as the ability to transmit pathogens. Better obtaining ...and integrating competence data into statistical models as covariates, as the response variable, and through postmodel validation should improve predictive research.
We present a framework to better understand and predict data-deficient and novel orthohantavirus traits based on three distinct orthohantavirus–rodent host groups: murid-borne, arvicoline-borne, and ...non-arvicoline cricetid-borne orthohantaviruses.Relative to other orthohantaviruses, cricetid orthohantaviruses often cause severe human disease, arvicoline orthohantaviruses cause mild disease, and murid orthohantavirus cause moderate disease.Murid orthohantaviruses are often transmitted through aerosolized excreta, arvicoline orthohantaviruses through aerosolized excreta and saliva, and cricetid orthohantaviruses through saliva.Murid and arvicoline orthohantaviruses generally have high host fidelity, but cricetid orthohantaviruses frequently spillover with possible multi-host systems.Our framework provides generalizable insight that can help inform public health and biosafety policy.
Orthohantaviruses present a global public health threat; there are 58 distinct viruses currently recognized and case fatality of pathogenic orthohantaviruses ranges from <0.1% to 50%. An Old World versus New World dichotomy is frequently applied to distinguish human diseases caused by orthohantaviruses. However, this geographic grouping masks the importance of phylogeny and virus–host ecology in shaping orthohantavirus traits, especially since related arvicoline rodents and their orthohantaviruses are found in both regions. We argue that orthohantaviruses can be separated into three phylogenetically based rodent host groups with differences in key functional traits, including human disease, transmission route, and virus–host fidelity. This framework can help understand and predict traits of under-studied and newly discovered orthohantaviruses and guide public health and biosafety policy.
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